Starting phenix.real_space_refine on Wed Feb 4 03:06:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dzf_47328/02_2026/9dzf_47328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dzf_47328/02_2026/9dzf_47328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dzf_47328/02_2026/9dzf_47328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dzf_47328/02_2026/9dzf_47328.map" model { file = "/net/cci-nas-00/data/ceres_data/9dzf_47328/02_2026/9dzf_47328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dzf_47328/02_2026/9dzf_47328.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.192 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 35 5.16 5 Cl 2 4.86 5 C 5360 2.51 5 N 1430 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8452 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3168 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 13, 'ARG:plan': 6, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 134 Chain: "B" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3137 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 15, 'ARG:plan': 7, 'ASN:plan1': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 156 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 939 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "L" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 2.22, per 1000 atoms: 0.26 Number of scatterers: 8452 At special positions: 0 Unit cell: (76.893, 102.885, 115.881, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 35 16.00 O 1625 8.00 N 1430 7.00 C 5360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.04 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG D 1 " - " ASN A 13 " " NAG E 1 " - " ASN A 395 " " NAG F 1 " - " ASN B 13 " " NAG G 1 " - " ASN B 395 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 360.3 milliseconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 34.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 19 through 35 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.512A pdb=" N LEU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 111 through 116 removed outlier: 3.539A pdb=" N PHE A 114 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 3.745A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 215 through 230 Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.739A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.688A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 315 through 338 removed outlier: 3.505A pdb=" N ALA A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 326 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'B' and resid 19 through 35 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 63 through 76 removed outlier: 3.556A pdb=" N LEU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 111 through 116 removed outlier: 3.646A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.771A pdb=" N GLY B 134 " --> pdb=" O TYR B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 266 through 274 removed outlier: 3.814A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 306 removed outlier: 3.707A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 314 No H-bonds generated for 'chain 'B' and resid 312 through 314' Processing helix chain 'B' and resid 315 through 338 removed outlier: 3.633A pdb=" N ALA B 319 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 325 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 326 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.582A pdb=" N ARG B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.534A pdb=" N GLY C 16 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN C 18 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.586A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.702A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 52 removed outlier: 9.104A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE A 81 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 189 removed outlier: 5.287A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE A 376 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN A 393 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 378 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 359 Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 52 removed outlier: 6.198A pdb=" N LEU B 3 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL B 49 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLY B 51 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL B 7 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N VAL B 80 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR B 4 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B 81 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.595A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE B 188 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 154 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 355 through 358 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.690A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.778A pdb=" N TYR H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.335A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.335A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2652 1.35 - 1.47: 2344 1.47 - 1.60: 3489 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 8539 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.14e+00 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.83e+00 bond pdb=" N GLN H 1 " pdb=" CA GLN H 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 8534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 11106 1.27 - 2.54: 442 2.54 - 3.81: 95 3.81 - 5.07: 23 5.07 - 6.34: 6 Bond angle restraints: 11672 Sorted by residual: angle pdb=" C CYS B 164 " pdb=" N PHE B 165 " pdb=" CA PHE B 165 " ideal model delta sigma weight residual 120.54 116.80 3.74 1.35e+00 5.49e-01 7.66e+00 angle pdb=" C CYS A 164 " pdb=" N PHE A 165 " pdb=" CA PHE A 165 " ideal model delta sigma weight residual 120.54 116.91 3.63 1.35e+00 5.49e-01 7.24e+00 angle pdb=" CB ARG L 93 " pdb=" CG ARG L 93 " pdb=" CD ARG L 93 " ideal model delta sigma weight residual 111.30 116.99 -5.69 2.30e+00 1.89e-01 6.12e+00 angle pdb=" C TRP A 379 " pdb=" N ASP A 380 " pdb=" CA ASP A 380 " ideal model delta sigma weight residual 122.59 126.26 -3.67 1.57e+00 4.06e-01 5.47e+00 angle pdb=" C3 BMA E 3 " pdb=" C2 BMA E 3 " pdb=" O2 BMA E 3 " ideal model delta sigma weight residual 112.95 106.61 6.34 3.00e+00 1.11e-01 4.47e+00 ... (remaining 11667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 4638 21.72 - 43.44: 334 43.44 - 65.16: 52 65.16 - 86.88: 25 86.88 - 108.60: 10 Dihedral angle restraints: 5059 sinusoidal: 1913 harmonic: 3146 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CA ARG L 93 " pdb=" C ARG L 93 " pdb=" N LYS L 94 " pdb=" CA LYS L 94 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual 180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 5056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1144 0.055 - 0.110: 146 0.110 - 0.165: 39 0.165 - 0.220: 2 0.220 - 0.274: 2 Chirality restraints: 1333 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA CYS B 164 " pdb=" N CYS B 164 " pdb=" C CYS B 164 " pdb=" CB CYS B 164 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1330 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 317 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO B 318 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 411 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 412 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 412 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 412 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 258 " 0.153 9.50e-02 1.11e+02 6.86e-02 3.06e+00 pdb=" NE ARG A 258 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 258 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 258 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 258 " 0.003 2.00e-02 2.50e+03 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 80 2.56 - 3.14: 6291 3.14 - 3.73: 12426 3.73 - 4.31: 19747 4.31 - 4.90: 32910 Nonbonded interactions: 71454 Sorted by model distance: nonbonded pdb=" O HOH H 311 " pdb=" O HOH H 317 " model vdw 1.971 3.040 nonbonded pdb=" OD1 ASP B 375 " pdb=" O HOH B1201 " model vdw 1.992 3.040 nonbonded pdb=" O HOH A1226 " pdb=" O HOH A1233 " model vdw 2.004 3.040 nonbonded pdb=" O HOH B1236 " pdb=" O HOH B1248 " model vdw 2.007 3.040 nonbonded pdb=" O HOH B1202 " pdb=" O HOH B1236 " model vdw 2.020 3.040 ... (remaining 71449 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 70 or (resid 71 and (nam \ e N or name CA or name C or name O or name CB )) or resid 72 through 118 or (res \ id 119 and (name N or name CA or name C or name O or name CB )) or resid 120 thr \ ough 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) \ or resid 185 through 191 or (resid 192 through 194 and (name N or name CA or nam \ e C or name O or name CB )) or resid 195 through 197 or (resid 198 and (name N o \ r name CA or name C or name O or name CB )) or resid 199 through 201 or (resid 2 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 203 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or r \ esid 233 through 260 or (resid 261 and (name N or name CA or name C or name O or \ name CB )) or resid 262 through 271 or (resid 272 through 273 and (name N or na \ me CA or name C or name O or name CB )) or resid 274 through 294 or (resid 295 a \ nd (name N or name CA or name C or name O or name CB )) or resid 296 through 345 \ or (resid 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 349 or (resid 350 and (name N or name CA or name C or name O or nam \ e CB )) or resid 351 through 409 or (resid 410 and (name N or name CA or name C \ or name O or name CB )) or resid 411 through 1101)) selection = (chain 'B' and (resid 1 through 44 or (resid 45 and (name N or name CA or name C \ or name O or name CB )) or resid 46 through 146 or (resid 147 through 148 and ( \ name N or name CA or name C or name O or name CB )) or resid 149 through 234 or \ (resid 235 and (name N or name CA or name C or name O or name CB )) or resid 236 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 through 384 or (resid 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 401 or (resid 402 through 403 and (name \ N or name CA or name C or name O or name CB )) or resid 404 through 422 or (res \ id 423 and (name N or name CA or name C or name O or name CB )) or resid 424 thr \ ough 1101)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8556 Z= 0.176 Angle : 0.643 6.646 11716 Z= 0.322 Chirality : 0.044 0.274 1333 Planarity : 0.005 0.069 1483 Dihedral : 16.698 108.602 3038 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.52 % Allowed : 13.03 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.25), residues: 1094 helix: 0.22 (0.29), residues: 330 sheet: -0.35 (0.28), residues: 305 loop : -1.09 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 258 TYR 0.014 0.001 TYR A 154 PHE 0.012 0.001 PHE B 172 TRP 0.009 0.001 TRP H 33 HIS 0.004 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8539) covalent geometry : angle 0.62382 (11672) SS BOND : bond 0.00940 ( 7) SS BOND : angle 2.91010 ( 14) hydrogen bonds : bond 0.14091 ( 359) hydrogen bonds : angle 6.88790 ( 1014) link_BETA1-4 : bond 0.00499 ( 6) link_BETA1-4 : angle 2.66084 ( 18) link_NAG-ASN : bond 0.00520 ( 4) link_NAG-ASN : angle 2.08396 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.339 Fit side-chains REVERT: B 309 MET cc_start: 0.7414 (mtp) cc_final: 0.7164 (mtp) outliers start: 4 outliers final: 4 residues processed: 107 average time/residue: 0.5818 time to fit residues: 66.1285 Evaluate side-chains 102 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain L residue 93 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 195 HIS A 249 GLN B 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.140862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125261 restraints weight = 7818.366| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 0.96 r_work: 0.3229 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8556 Z= 0.160 Angle : 0.639 6.283 11716 Z= 0.321 Chirality : 0.044 0.147 1333 Planarity : 0.005 0.053 1483 Dihedral : 9.508 68.430 1416 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.35 % Allowed : 11.87 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.25), residues: 1094 helix: 1.16 (0.29), residues: 330 sheet: -0.28 (0.28), residues: 305 loop : -1.01 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.010 0.001 TYR A 154 PHE 0.012 0.002 PHE B 172 TRP 0.010 0.001 TRP L 92 HIS 0.006 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8539) covalent geometry : angle 0.62528 (11672) SS BOND : bond 0.00835 ( 7) SS BOND : angle 1.90679 ( 14) hydrogen bonds : bond 0.04900 ( 359) hydrogen bonds : angle 5.00359 ( 1014) link_BETA1-4 : bond 0.00659 ( 6) link_BETA1-4 : angle 2.58993 ( 18) link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 2.08970 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.340 Fit side-chains REVERT: A 249 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7896 (mp10) outliers start: 26 outliers final: 11 residues processed: 115 average time/residue: 0.5697 time to fit residues: 69.6315 Evaluate side-chains 107 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 93 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.142319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.127638 restraints weight = 7737.745| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 0.88 r_work: 0.3207 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8556 Z= 0.129 Angle : 0.588 6.686 11716 Z= 0.296 Chirality : 0.043 0.147 1333 Planarity : 0.005 0.052 1483 Dihedral : 7.864 59.268 1414 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.71 % Allowed : 13.94 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1094 helix: 1.43 (0.29), residues: 332 sheet: -0.20 (0.28), residues: 308 loop : -1.03 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 258 TYR 0.014 0.001 TYR A 154 PHE 0.011 0.001 PHE B 172 TRP 0.009 0.001 TRP L 92 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8539) covalent geometry : angle 0.57465 (11672) SS BOND : bond 0.00608 ( 7) SS BOND : angle 1.82176 ( 14) hydrogen bonds : bond 0.04285 ( 359) hydrogen bonds : angle 4.76703 ( 1014) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 2.42564 ( 18) link_NAG-ASN : bond 0.00381 ( 4) link_NAG-ASN : angle 1.98605 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.240 Fit side-chains REVERT: A 271 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8096 (tpt90) REVERT: B 149 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8227 (tt0) REVERT: B 309 MET cc_start: 0.7891 (mtp) cc_final: 0.7606 (mtp) REVERT: L 93 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8309 (mmt180) outliers start: 21 outliers final: 11 residues processed: 114 average time/residue: 0.5373 time to fit residues: 65.4325 Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 149 GLN Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 93 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 53 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.129967 restraints weight = 7934.841| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 0.83 r_work: 0.3243 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8556 Z= 0.117 Angle : 0.558 7.489 11716 Z= 0.280 Chirality : 0.042 0.142 1333 Planarity : 0.004 0.050 1483 Dihedral : 6.627 55.243 1414 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 14.06 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1094 helix: 1.58 (0.29), residues: 332 sheet: -0.09 (0.28), residues: 308 loop : -1.03 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.011 0.001 TYR A 154 PHE 0.011 0.001 PHE B 172 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8539) covalent geometry : angle 0.54436 (11672) SS BOND : bond 0.00606 ( 7) SS BOND : angle 2.01309 ( 14) hydrogen bonds : bond 0.03912 ( 359) hydrogen bonds : angle 4.60453 ( 1014) link_BETA1-4 : bond 0.00591 ( 6) link_BETA1-4 : angle 2.21377 ( 18) link_NAG-ASN : bond 0.00373 ( 4) link_NAG-ASN : angle 1.84628 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.329 Fit side-chains REVERT: A 373 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: L 11 LEU cc_start: 0.8439 (tp) cc_final: 0.8001 (tt) outliers start: 26 outliers final: 10 residues processed: 118 average time/residue: 0.5305 time to fit residues: 66.8434 Evaluate side-chains 110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.0570 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.134490 restraints weight = 8315.091| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.33 r_work: 0.3488 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8556 Z= 0.121 Angle : 0.558 6.996 11716 Z= 0.281 Chirality : 0.042 0.155 1333 Planarity : 0.004 0.049 1483 Dihedral : 6.109 55.143 1409 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.84 % Allowed : 14.71 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1094 helix: 1.67 (0.29), residues: 332 sheet: -0.01 (0.28), residues: 308 loop : -1.00 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.013 0.001 TYR A 154 PHE 0.010 0.001 PHE B 172 TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8539) covalent geometry : angle 0.54579 (11672) SS BOND : bond 0.00620 ( 7) SS BOND : angle 1.88276 ( 14) hydrogen bonds : bond 0.03943 ( 359) hydrogen bonds : angle 4.55611 ( 1014) link_BETA1-4 : bond 0.00548 ( 6) link_BETA1-4 : angle 2.05009 ( 18) link_NAG-ASN : bond 0.00363 ( 4) link_NAG-ASN : angle 1.85752 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.210 Fit side-chains REVERT: A 162 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7221 (mt-10) REVERT: A 373 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: B 309 MET cc_start: 0.7751 (mtp) cc_final: 0.7513 (mtm) outliers start: 22 outliers final: 12 residues processed: 115 average time/residue: 0.4343 time to fit residues: 53.3672 Evaluate side-chains 112 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.154975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134235 restraints weight = 8236.484| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.31 r_work: 0.3484 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8556 Z= 0.125 Angle : 0.562 7.177 11716 Z= 0.283 Chirality : 0.042 0.164 1333 Planarity : 0.004 0.048 1483 Dihedral : 5.892 55.328 1409 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.10 % Allowed : 15.35 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1094 helix: 1.70 (0.29), residues: 332 sheet: 0.02 (0.28), residues: 308 loop : -1.01 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.012 0.001 TYR A 154 PHE 0.011 0.001 PHE B 172 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8539) covalent geometry : angle 0.55034 (11672) SS BOND : bond 0.00674 ( 7) SS BOND : angle 1.90543 ( 14) hydrogen bonds : bond 0.04018 ( 359) hydrogen bonds : angle 4.53637 ( 1014) link_BETA1-4 : bond 0.00537 ( 6) link_BETA1-4 : angle 1.98227 ( 18) link_NAG-ASN : bond 0.00337 ( 4) link_NAG-ASN : angle 1.90415 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.224 Fit side-chains REVERT: A 252 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 271 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8067 (tpt-90) REVERT: A 373 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7398 (mm-30) REVERT: B 309 MET cc_start: 0.7818 (mtp) cc_final: 0.7473 (mtp) REVERT: L 11 LEU cc_start: 0.8303 (tp) cc_final: 0.7826 (tt) outliers start: 24 outliers final: 13 residues processed: 115 average time/residue: 0.5064 time to fit residues: 62.0030 Evaluate side-chains 116 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 6.9990 chunk 98 optimal weight: 0.0030 chunk 50 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127067 restraints weight = 7878.530| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 0.83 r_work: 0.3202 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8556 Z= 0.170 Angle : 0.633 7.024 11716 Z= 0.317 Chirality : 0.045 0.187 1333 Planarity : 0.005 0.048 1483 Dihedral : 6.102 57.261 1409 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.87 % Allowed : 15.10 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1094 helix: 1.55 (0.29), residues: 332 sheet: -0.03 (0.28), residues: 308 loop : -1.06 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.012 0.002 TYR A 154 PHE 0.015 0.002 PHE A 165 TRP 0.013 0.002 TRP L 92 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8539) covalent geometry : angle 0.61940 (11672) SS BOND : bond 0.00941 ( 7) SS BOND : angle 2.45989 ( 14) hydrogen bonds : bond 0.04811 ( 359) hydrogen bonds : angle 4.68101 ( 1014) link_BETA1-4 : bond 0.00515 ( 6) link_BETA1-4 : angle 2.11792 ( 18) link_NAG-ASN : bond 0.00305 ( 4) link_NAG-ASN : angle 2.09837 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.300 Fit side-chains REVERT: A 252 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: A 271 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8206 (tpt-90) REVERT: A 373 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: B 309 MET cc_start: 0.7885 (mtp) cc_final: 0.7525 (mtp) outliers start: 30 outliers final: 16 residues processed: 117 average time/residue: 0.5719 time to fit residues: 71.2236 Evaluate side-chains 110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128238 restraints weight = 7807.886| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 0.81 r_work: 0.3215 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8556 Z= 0.144 Angle : 0.593 6.599 11716 Z= 0.300 Chirality : 0.043 0.195 1333 Planarity : 0.005 0.048 1483 Dihedral : 5.968 56.631 1409 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.35 % Allowed : 15.61 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.25), residues: 1094 helix: 1.61 (0.29), residues: 332 sheet: 0.02 (0.28), residues: 308 loop : -1.05 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 355 TYR 0.013 0.001 TYR A 154 PHE 0.013 0.001 PHE A 165 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8539) covalent geometry : angle 0.57935 (11672) SS BOND : bond 0.00745 ( 7) SS BOND : angle 2.38775 ( 14) hydrogen bonds : bond 0.04364 ( 359) hydrogen bonds : angle 4.63399 ( 1014) link_BETA1-4 : bond 0.00526 ( 6) link_BETA1-4 : angle 2.02283 ( 18) link_NAG-ASN : bond 0.00345 ( 4) link_NAG-ASN : angle 2.06726 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.331 Fit side-chains REVERT: A 162 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: A 252 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: A 271 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8199 (tpt-90) REVERT: A 373 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: B 309 MET cc_start: 0.7917 (mtp) cc_final: 0.7528 (mtp) REVERT: H 57 TYR cc_start: 0.8873 (m-80) cc_final: 0.8672 (m-80) outliers start: 26 outliers final: 17 residues processed: 109 average time/residue: 0.5920 time to fit residues: 68.6565 Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 chunk 78 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134562 restraints weight = 8283.368| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.37 r_work: 0.3491 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8556 Z= 0.112 Angle : 0.538 6.431 11716 Z= 0.272 Chirality : 0.041 0.163 1333 Planarity : 0.004 0.047 1483 Dihedral : 5.609 54.828 1409 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.35 % Allowed : 15.74 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1094 helix: 1.75 (0.29), residues: 332 sheet: 0.10 (0.29), residues: 308 loop : -1.00 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 355 TYR 0.014 0.001 TYR A 154 PHE 0.011 0.001 PHE B 172 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8539) covalent geometry : angle 0.52645 (11672) SS BOND : bond 0.00526 ( 7) SS BOND : angle 1.84339 ( 14) hydrogen bonds : bond 0.03714 ( 359) hydrogen bonds : angle 4.48873 ( 1014) link_BETA1-4 : bond 0.00528 ( 6) link_BETA1-4 : angle 1.84340 ( 18) link_NAG-ASN : bond 0.00342 ( 4) link_NAG-ASN : angle 1.88628 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.239 Fit side-chains REVERT: A 162 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: A 203 MET cc_start: 0.7074 (tpp) cc_final: 0.6621 (tpp) REVERT: A 252 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7983 (tt0) REVERT: A 271 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8054 (tpt-90) REVERT: A 373 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: B 309 MET cc_start: 0.7843 (mtp) cc_final: 0.7500 (mtp) REVERT: H 57 TYR cc_start: 0.8864 (m-80) cc_final: 0.8639 (m-80) REVERT: L 11 LEU cc_start: 0.8209 (tp) cc_final: 0.7756 (tt) outliers start: 26 outliers final: 14 residues processed: 116 average time/residue: 0.5650 time to fit residues: 69.7151 Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 12 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134252 restraints weight = 8249.298| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.32 r_work: 0.3480 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8556 Z= 0.129 Angle : 0.570 7.022 11716 Z= 0.289 Chirality : 0.043 0.179 1333 Planarity : 0.004 0.048 1483 Dihedral : 5.683 55.759 1409 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.97 % Allowed : 16.52 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1094 helix: 1.72 (0.29), residues: 332 sheet: 0.11 (0.29), residues: 308 loop : -1.00 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 355 TYR 0.013 0.001 TYR A 154 PHE 0.012 0.001 PHE A 165 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8539) covalent geometry : angle 0.55679 (11672) SS BOND : bond 0.00661 ( 7) SS BOND : angle 2.41660 ( 14) hydrogen bonds : bond 0.04029 ( 359) hydrogen bonds : angle 4.52220 ( 1014) link_BETA1-4 : bond 0.00520 ( 6) link_BETA1-4 : angle 1.87322 ( 18) link_NAG-ASN : bond 0.00297 ( 4) link_NAG-ASN : angle 1.93572 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.426 Fit side-chains REVERT: A 203 MET cc_start: 0.7105 (tpp) cc_final: 0.6649 (tpp) REVERT: A 252 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: A 271 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8080 (tpt-90) REVERT: A 373 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7415 (mm-30) REVERT: B 309 MET cc_start: 0.7870 (mtp) cc_final: 0.7564 (mtp) REVERT: L 11 LEU cc_start: 0.8204 (tp) cc_final: 0.7742 (tt) outliers start: 23 outliers final: 15 residues processed: 116 average time/residue: 0.5901 time to fit residues: 72.9110 Evaluate side-chains 114 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 45 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.139728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124656 restraints weight = 7764.146| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.89 r_work: 0.3180 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8556 Z= 0.207 Angle : 0.693 10.619 11716 Z= 0.349 Chirality : 0.047 0.305 1333 Planarity : 0.005 0.048 1483 Dihedral : 6.233 58.562 1409 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.97 % Allowed : 16.52 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.25), residues: 1094 helix: 1.42 (0.29), residues: 332 sheet: 0.01 (0.28), residues: 308 loop : -1.09 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 355 TYR 0.012 0.002 TYR A 154 PHE 0.018 0.002 PHE A 165 TRP 0.017 0.002 TRP L 92 HIS 0.006 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00514 ( 8539) covalent geometry : angle 0.67182 (11672) SS BOND : bond 0.01124 ( 7) SS BOND : angle 3.98132 ( 14) hydrogen bonds : bond 0.05320 ( 359) hydrogen bonds : angle 4.79575 ( 1014) link_BETA1-4 : bond 0.00505 ( 6) link_BETA1-4 : angle 2.14549 ( 18) link_NAG-ASN : bond 0.00279 ( 4) link_NAG-ASN : angle 2.21451 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.44 seconds wall clock time: 47 minutes 57.52 seconds (2877.52 seconds total)